Assessment of genetic diversity in aquaculture stocks is essential for maintaining breeding efficiency and preventing genetic erosion in selectively bred fish populations. This study applied inter-simple sequence repeat polymerase chain reaction (ISSR-PCR) markers to evaluate the genetic structure and diversity of the Antoniny–Zozulenets intrabreed type of Ukrainian scaly and leather carp reared at the “Stara Syniava” fish farm. Five trinucleotide ISSR primers ((CTC)6C, (GAG)6C, (AGC)6G, (ACC)6G, (AGC)6C) were used for molecular genetic analysis. A total of 132 DNA fragments were amplified, of which 72.3 % were polymorphic, indicating a considerable level of genetic variability within the studied stocks. The informativeness of the ISSR markers was assessed using polymorphic information content (PIC), percentage of polymorphic bands (PPB), effective multiplex ratio (EMR), marker index (MI), and resolving power (Rp). The mean values of these parameters were PIC=0.123, PPB=72. %, EMR=19.1, MI=2.3, and Rp=9.6, demonstrating the effectiveness of the selected marker system for population genetic analysis. The sizes of amplified DNA fragments ranged from 150 to 1170 bp depending on the primer used. Genetic diversity indices showed moderate variation between the studied groups: Shannon’s index reached 0.265±0.017 in leather carp and 0.242±0.018 in scaly carp, while unbiased expected heterozygosity was 0.155±0.011 and 0.144±0.012, respectively. The average number of alleles per locus (Na) was 1.571±0.072 in leather carp and 1.334±0.082 in scaly carp, with effective allele numbers (Ne) of 1.216±0.019 and 1.201±0.019. These results demonstrate that ISSR markers provide a reliable tool for genotyping and monitoring genetic variability in Ukrainian carp populations and can support selective breeding and conservation programs.
